There's a bug with defraggler where a large file that is "defragmented" around some unmovable files (ie. $MFT) seems to overly fragment them instead.
For example the file X where U is the unmovable file. Rather than splitting it into two contiguous segments either side of U, it somehow gets “defragmented” into hundreds of fragments on full disk defrag, even though it’s occupying a contiguous area on the disk, it’s all in fragments out of order.
XXXUXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
I have observed this on a number of occasions any time Defraggler places a large file around unmovable files.